LAMMPS (30 Jul 2021) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 2.8700001 2.8700001 2.8700001 Created orthogonal box = (0.0000000 -29.271243 0.0000000) to (25.347154 29.271243 4.9709860) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.5494892 4.5028266 4.9709860 Created 317 atoms using lattice units in orthogonal box = (0.0000000 -29.271243 0.0000000) to (25.347154 29.271243 4.9709860) create_atoms CPU = 0.002 seconds 317 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.5494892 4.5028266 4.9709860 Created 316 atoms using lattice units in orthogonal box = (0.0000000 -29.271243 0.0000000) to (25.347154 29.271243 4.9709860) create_atoms CPU = 0.001 seconds 316 atoms in group lower Displacing atoms ... System init for delete_atoms ... Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 9 20 2 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair kim, perpetual attributes: full, newton off, cut 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 10 atoms, new total = 623 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM: https://doi.org/10.1007/s11837-011-0102-6 - OpenKIM potential: https://openkim.org/cite/MO_024705128470_000#item-citation The log file lists these citations in BibTeX format. CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 9 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.494 | 4.494 | 4.494 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2576.1684 0 -2576.1684 33607.986 91 0 -2645.6473 0 -2645.6473 11009.965 Loop time of 0.760234 on 1 procs for 91 steps with 623 atoms 98.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2576.16839859351 -2645.64514409471 -2645.64733099018 Force two-norm initial, final = 81.857090 0.16830401 Force max component initial, final = 21.163894 0.061259550 Final line search alpha, max atom move = 1.0000000 0.061259550 Iterations, force evaluations = 91 176 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.73453 | 0.73453 | 0.73453 | 0.0 | 96.62 Neigh | 0.0069643 | 0.0069643 | 0.0069643 | 0.0 | 0.92 Comm | 0.0094494 | 0.0094494 | 0.0094494 | 0.0 | 1.24 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009294 | | | 1.22 Nlocal: 623.000 ave 623 max 623 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3179.00 ave 3179 max 3179 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 41720.0 ave 41720 max 41720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 41720 Ave neighs/atom = 66.966292 Neighbor list builds = 1 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 9 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 91 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.495 | 4.495 | 4.495 Mbytes Step Temp E_pair E_mol TotEng Press Volume 91 0 -2645.6473 0 -2645.6473 11009.965 7376.3736 95 0 -2645.7717 0 -2645.7717 2571.5054 7414.2163 Loop time of 0.0263779 on 1 procs for 4 steps with 623 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2645.64733099017 -2645.77094288981 -2645.77173017964 Force two-norm initial, final = 66.961563 1.2989307 Force max component initial, final = 56.087419 1.2834872 Final line search alpha, max atom move = 0.00020834226 0.00026740463 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.02472 | 0.02472 | 0.02472 | 0.0 | 93.71 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00030644 | 0.00030644 | 0.00030644 | 0.0 | 1.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001352 | | | 5.12 Nlocal: 623.000 ave 623 max 623 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3157.00 ave 3157 max 3157 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 41738.0 ave 41738 max 41738 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 41738 Ave neighs/atom = 66.995185 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 9 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.633 | 4.633 | 4.633 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2645.7717 0 -2645.7717 2571.5054 Loop time of 3.03e-06 on 1 procs for 0 steps with 623 atoms 132.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 3.03e-06 | | |100.00 Nlocal: 623.000 ave 623 max 623 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3126.00 ave 3126 max 3126 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 41624.0 ave 41624 max 41624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 41624 Ave neighs/atom = 66.812199 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 9 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.633 | 4.633 | 4.633 Mbytes Step v_pe_metal c_particle_engsum v_lx_metal v_ly_metal v_lz_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_mindist_metal v_csymsum_metal 0 -2645.7717 -2645.7717 25.39267 58.542486 4.9875322 2571.5054 2571.5054 -277.85347 7989.7914 2.5782905 2.2896801 636.54834 Loop time of 2.877e-06 on 1 procs for 0 steps with 623 atoms 139.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 2.877e-06 | | |100.00 Nlocal: 623.000 ave 623 max 623 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3126.00 ave 3126 max 3126 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 20812.0 ave 20812 max 20812 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 41624.0 ave 41624 max 41624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 41624 Ave neighs/atom = 66.812199 Neighbor list builds = 0 Dangerous builds = 0 623 -2645.77166787964 eV 2.28968008796992 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01